---
name: "segmentFst"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/segmentFst"
---

# segmentFst(1)

## NAME

**segmentFst**

## SYNOPSIS

**segmentFst** -s 0.7 -f wcFst.output.txt

## DESCRIPTION

**segmentFst** creates genomic segments (bed file) for regions with high wcFst

## OPTIONS

-

  ```
  **segmentFst** provides a way to find continious regions with high Fst values.  It takes the output of wcFst and produces a BED file.  These high Fst region can be permutated with 'permuteGPATwindow'
  Output : 8 columns :
       1. Seqid
       2. Start (zero based)
       3. End   (zero based)
       4. Average Fst
       5. Average high Fst (Fst > -s)
       6. N Fst values in segment
       7. N high fst values in segment
       8. Segment length
  required: -f            -- Output from wcFst
  optional: -s            -- High Fst cutoff [0.8]
  Type: statistics
  ```

## EXIT VALUES

- **0**

  Success

- **not 0**

  Failure

## SEE ALSO

[**vcflib**(1)](/vcflib/1.md)

## OTHER

## LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

## AUTHORS

Erik Garrison and vcflib contributors.